Zinc in PDB 5jjr: Dengue 3 NS5 Protein with Compound 29

The structure of Dengue 3 NS5 Protein with Compound 29, PDB code: 5jjr was solved by J.Lescar, A.El Sahili, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.30 / 1.99
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.600, 150.370, 69.140, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22.5

The structure of Dengue 3 NS5 Protein with Compound 29 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Dengue 3 NS5 Protein with Compound 29 (pdb code 5jjr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Dengue 3 NS5 Protein with Compound 29, PDB code: 5jjr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Dengue 3 NS5 Protein with Compound 29


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dengue 3 NS5 Protein with Compound 29 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:15.7 occ:1.00 OE2 A:GLU437 2.1 13.9 1.0 NE2 A:HIS441 2.2 15.1 1.0 SG A:CYS446 2.3 20.3 1.0 SG A:CYS449 2.3 18.6 1.0 CB A:CYS449 3.0 15.7 1.0 CD A:GLU437 3.1 13.3 1.0 CD2 A:HIS441 3.1 15.5 1.0 CE1 A:HIS441 3.2 15.0 1.0 CB A:CYS446 3.4 16.7 1.0 CG A:GLU437 3.4 21.7 1.0 N A:CYS449 3.7 16.2 1.0 CA A:CYS446 3.8 17.2 1.0 CA A:CYS449 3.9 15.8 1.0 N A:GLY447 4.2 17.5 1.0 OE1 A:GLU437 4.2 12.9 1.0 CG A:HIS441 4.3 16.7 1.0 ND1 A:HIS441 4.3 16.7 1.0 N A:SER448 4.3 16.1 1.0 C A:CYS446 4.4 20.0 1.0 CG2 A:THR571 4.4 19.7 1.0 O A:HOH1359 4.5 12.7 1.0 C A:SER448 4.6 21.6 1.0 CD1 A:LEU483 4.8 8.4 1.0 O A:LYS445 4.8 19.3 1.0 CB A:GLU437 4.9 12.4 1.0 O A:HOH1335 5.0 19.1 1.0

Zinc binding site 2 out of 2 in the Dengue 3 NS5 Protein with Compound 29


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dengue 3 NS5 Protein with Compound 29 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:21.2 occ:1.00 NE2 A:HIS712 2.0 16.7 1.0 CE1 A:HIS714 2.1 23.9 1.0 SG A:CYS847 2.4 21.1 1.0 SG A:CYS728 2.4 16.4 1.0 NE2 A:HIS714 2.8 24.7 1.0 CE1 A:HIS712 2.9 16.8 1.0 CD2 A:HIS712 3.0 16.7 1.0 CB A:CYS728 3.2 13.3 1.0 ND1 A:HIS714 3.2 24.2 1.0 CB A:CYS847 3.3 17.9 1.0 ND1 A:HIS712 4.1 16.9 1.0 CD2 A:HIS714 4.1 24.5 1.0 CG A:HIS712 4.1 15.4 1.0 CD1 A:LEU839 4.2 17.4 1.0 CG A:HIS714 4.3 22.7 1.0 CA A:CYS728 4.4 12.8 1.0 O A:HOH1534 4.5 31.1 1.0 O A:HOH1490 4.5 28.6 1.0 C A:CYS728 4.5 18.7 1.0 O A:HOH1544 4.6 35.5 1.0 NH1 A:ARG769 4.6 15.7 1.0 N A:ARG729 4.6 15.8 1.0 CA A:CYS847 4.7 19.7 1.0

S.P.Lim, C.G.Noble, C.C.Seh, T.S.Soh, A.El Sahili, G.K.Chan, J.Lescar, R.Arora, T.Benson, S.Nilar, U.Manjunatha, K.F.Wan, H.Dong, X.Xie, P.Y.Shi, F.Yokokawa. Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling Plos Pathog. V. 12 05737 2016.
ISSN: ESSN 1553-7374
PubMed: 27500641
DOI: 10.1371/JOURNAL.PPAT.1005737